update docs and Dockerfile

Dockerfile

@@ -10,13 +10,6 @@ LABEL "maintainer"="jorge.mendesdejesus@isric.org"
 ENV LANG=C.UTF-8 LC_ALL=C.UTF-8
 ENV DEBIAN_FRONTEND noninteractive
 
-ENV DB_HOST scomp1270.wurnet.nl
-ENV DB_NAME isric
-ENV DB_USER hass005
-ENV DB_PASSWORD 1515NewPW
-ENV DB_PORT 5479
-ENV MONOLITH_PATH /data/monoliths
-
 RUN apt-get update \
       && apt-get install -y --no-install-recommends postgresql-client build-essential libpq-dev tini
 

README.md

-WSM
----
+# WSM
 
 World Soil Museum - REST API
 
-App structure
--------------
+## App structure
 
 REST APP is on [appWSM.py](./appWSM.py) and then calling modules like `resources`. This app is based on:
 
@@ -25,18 +23,23 @@ App accesses ISRIC database on `scomp1270.wurnet.nl`.
 
 **NOTE:** To copy files check section below  [Monolith picture location](#monolith-picture-location)
 
+### DB access configuration / Data path
 
-### DB access configuration
+DB options and monolith path location is picked up from env variables on script: [common/secret.py](./common/secret.py).
 
-DB options are picked up from file [common/secret.py](./common/secret.py). This file needs to be changed if a new DB is used.
-
-NOTE: Jorge did a bad job on leaving DB password on the repository. Password should be on envs.
+```bash
+DB_HOST=scomp1270.wurnet.nl
+DB_NAME=isric
+DB_USER=hass005
+DB_PASSWORD=<removed>
+DB_PORT=5479
+MONOLITH_PATH=/data/monolith
+```
 
 ### DB queries
 
  In the code we have the following queries:
 
-
 | code path         | method/function        | SQL                          |
 |:-----------------:|:---------------------:|:-----------------------------:|
 | common/filters.py | filter_classification()|select * from web_isis.vw_isis_profiles_with_classification_geo_img_rest where classification ilike %s"|
@@ -44,40 +47,35 @@ NOTE: Jorge did a bad job on leaving DB password on the repository. Password sho
 
 **NOTE:** Views need to be refreshed when new data is added to the upstream tables
 
-Monolith picture location
--------------------------
+### Monolith picture location
 
 Monoliths used by REST are stored on ISRIC data volume, the access to this volume is very restricted and based on IP. Rserver (scomp1457.wurnet.nl), on this server users haas005, turku001 and ruipe001 have a symbolic link to the monoliths.
 
 There the monolith pictures can be updated or modified
 
-Monolith file copy 
-------------------
+### Monolith file copy
 
 On the Rserver is it better to copy the monoliths from workspace scratch into `ISRIC_Monoliths`. On the home folder of user the command would look like:
 
-```
+```bash
 turdu001@scomp1457:~$ cp -rv ./ISRIC_Workspace/scratch/Upload_ToRest/combined_processed/* ./ISRIC_Monoliths/ 
 ```
 
 The FB-IT mounts are not reliable, check if "ISRIC_Monolith" is accessible, it not mount it:
 
-```
+```bash
 # mount all volumes from /etc/fstab
 sudo mount -a
 ```
 
 In case of batch file permission it is advisable (NOTE: Only sudo can do it):
 
-```
+```bash
 find /mnt/ISRIC_Monoliths -type d -exec chmod 777 {} \; #for directories
 find /mnt/ISRIC_Monoliths -type f -exec chmod 666 {} \; #for files
 ```
 
-
-
-Monolith image update and implementation
-----------------------------------------
+## Monolith image update and implementation
 
 To update monolith images, it is necessary:
 
@@ -89,8 +87,7 @@ It is advisable to use a rsync software when moving files around.
 
 REST API doesn't make any assumptions on files and will crawl the fold structure for the pictures. It maybe necessary some code changes if there are to many changes.
 
-Local Deployment
-----------------
+## Local Deployment
 
 This API can be deployed using a docker container. The code resides in the
 host system, together with the monoliths images to be served. These images
@@ -100,38 +97,45 @@ as this file). This code folder is then mapped into the container at startup.
 The Dockerfile present in this project sets up the API with Gunicorn and nginx.
 To build the container image change to the project folder and run:
 
-`docker build -t ldesousa/wsm.rest .`
+`docker build -t wsm.rest .`
+
+The resulting image is named `wsm/rest`.
 
-The resulting image is named `ldesousa/wsm.rest`. 
-To run the image it is necessary to map the right environment variables to connect to the database as well as mount the source code folder and bind port 80 (where nginx listens):
+To run the image it is necessary to map the right environment variables to connect to the database as well as mount the source code folder and bind port 8000 (where gunicorn listens):
 
 Docker run command with envfile:
+
 ```bash
-docker run -dit --env-file /path/to/envfile -v /data/monoliths:/data/monoliths --name wsm.rest -p 8081:80 ldesousa/wsm.rest
+docker run -dit \
+   --env-file /path/to/envfile \
+   -v /data/monoliths:/data/monoliths \
+   --name wsm.rest -p 8000:8000 wsm.rest
 ```
+
 Docker run command with variables inline:
+
 ```bash
-docker run -dit -e DB_HOST=scomp1270.wurnet.nl -e DB_NAME=isric  -e DB_USER=haas005  -e DB_PASSWORD=wur -e DB_PORT=5479 -v /data/monoliths:/data/monoliths --name wsm.rest -p 8081:80 ldesousa/wsm.rest
+docker run -dit \
+    -e DB_HOST=scomp1270.wurnet.nl \
+    -e DB_NAME=isric \ 
+    -e DB_USER=haas005 \
+    -e DB_PASSWORD=<REMOVED>
+    -e MONOLITH_PATH=/data/monolith 
+    -e DB_PORT=5479 \
+    -v /data/monoliths:/data/monoliths 
+    --name wsm.rest -p 8000:8000 wsm.rest
 ```
 
-Your container will now be available on [localhost:8081](http://localhost:8081)
-
-OC deployment
-=============
-
-OC uses the gitlab webhook to deploy the application on project `isric-files`. Pod application is named `rest-wsm`, and external route is `rest-wsm.isric.org`.
+Your container will now be available on [localhost:8000](http://localhost:8000)
 
-Image build is based on the `python3.6` OC image `openshift/python:3.6` and WSGI system is configure with envs:
+## K8s deployment
 
-```
-APP_MODULE=appWSM:app
-```
+- `ENV` variables are set as k8s secrets on the [ISRIC deployment repository](https://git.wur.nl/isric/ict/k8s-deployments)
 
-Envs are stored on configuration file [here](.s2i/environment)
+- Application follows the standard k8s deployment.
 
-Pod mounts the `isric-files/monoliths` on  `/opt/app-root/src/monoliths (ro)`
+- TODO: Write about semanatic tagging
 
-Image processing and metadata
-=============================
+## Image processing and metadata
 
 Please consult the specific folder **[README](imageProcessing/README.md)**

common/secret.py.dist

-"""Password of database"""
-"""This is just an example, change to the correct values and rename the file to
-   secret.py"""
-DB={"host":"85.214.241.121","database":"isric", "user":"isis", "password":"@#%951GHKaef"}
\ No newline at end of file